Create an object of class gDataMPP — createGDataMPP • statgenMPP

Function for creating an object of class gDataMPP from an object of class IBDprob (computed or imported using statgenIBD) and phenotypic data.

Usage

createGDataMPP(IBDprob, pheno)

Arguments

IBDprob: An object of class IBDprob.
pheno: A data frame with at least columns "genotype" for the "genotype" and one or more numerical columns containing phenotypic information. A column "cross" can be used for indicating the cross the genotype comes from. This column is ignored if the IBDprob has an attribute genoCross containing this information (the default behaviour).

Value

An object of class gDataMPP

Examples

## Read phenotypic data.
pheno <- read.delim(system.file("extdata/multipop", "AxBxCpheno.txt",
                               package = "statgenMPP"))
## Rename first column to genotype.
colnames(pheno)[1] <- "genotype"

## Compute IBD probabilities for simulated population using statgenIBD - AxB
AB <- statgenIBD::calcIBD(popType = "F4DH",
                         markerFile = system.file("extdata/multipop", "AxB.txt",
                                                 package = "statgenMPP"),
                         mapFile = system.file("extdata/multipop", "mapfile.txt",
                                              package = "statgenMPP"),
                         evalDist = 5)

## Create an object of class gDataMPP from IBD probabilities and
## phenotypic data.
ABMPP <- createGDataMPP(IBDprob = AB, pheno = pheno)